1.Artificial intelligence-driven multi-omics approaches in Alzheimer's disease: Progress, challenges, and future directions.
Fang REN ; Jing WEI ; Qingxin CHEN ; Mengling HU ; Lu YU ; Jianing MI ; Xiaogang ZHOU ; Dalian QIN ; Jianming WU ; Anguo WU
Acta Pharmaceutica Sinica B 2025;15(9):4327-4385
Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by cognitive decline and memory loss, with few effective treatments currently available. The multifactorial nature of AD, shaped by genetic, environmental, and biological factors, complicates both research and clinical management. Recent advances in artificial intelligence (AI) and multi-omics technologies provide new opportunities to elucidate the molecular mechanisms of AD and identify early biomarkers for diagnosis and prognosis. AI-driven approaches such as machine learning, deep learning, and network-based models have enabled the integration of large-scale genomic, transcriptomic, proteomic, metabolomic, and microbiomic datasets. These efforts have facilitated the discovery of novel molecular signatures and therapeutic targets. Methods including deep belief networks and joint deep semi-non-negative matrix factorization have contributed to improvements in disease classification and patient stratification. However, ongoing challenges remain. These include data heterogeneity, limited interpretability of complex models, a lack of large and diverse datasets, and insufficient clinical validation. The absence of standardized multi-omics data processing methods further restricts progress. This review systematically summarizes recent advances in AI-driven multi-omics research in AD, highlighting achievements in early diagnosis and biomarker discovery while discussing limitations and future directions needed to advance these approaches toward clinical application.
2.Application value of serum bromodomain-containing protein 4 combined with gastrin-17 in diagnosis of Helicobacter pylori-positive early gastric cancer
Ting XIE ; Chengguo REN ; Yunxia LIN ; Shibin WANG ; Long LI ; Jianming SU ; Wen CAO
Journal of Clinical Medicine in Practice 2025;29(13):50-54
Objective To investigate the diagnostic value of serum bromodomain-containing pro-tein 4(BRD4)combined with gastrin-17(G-17)in Helicobacter pylori(Hp)-positive early gastric cancer.Methods A total of 88 patients with Hp-positive early gastric cancer admitted to our hospital from September 2021 to September 2023 were selected as early gastric cancer group.Meanwhile,92 patients with Hp-positive precancerous lesions and 80 patients with Hp-positive gastritis admitted dur-ing the same period were selected as precancerous lesion group and gastritis group,respectively.En-zyme-linked immunosorbent assay(ELISA)was used to detect the serum levels of BRD4 and G-17.Multivariate logistic regression analysis was performed to screen the influencing factors of Hp-positive early gastric cancer.Receiver operating characteristic(ROC)curve analysis was used to evaluate the diagnostic value of serum BRD4 and G-17 in Hp-positive early gastric cancer.Results Compared with the gastritis group,the levels of BRD4 and G-17 in the precancerous lesion group and early gastric cancer group were significantly increased(P<0.05).Furthermore,compared with the precancerous le-sion group,the levels of BRD4 and G-17 in the early gastric cancer group were also significantly elevated(P<0.05).The proportion of patients with a family history of gastric cancer,those who preferred hot food,cold food,or high-salt food,as well as the levels of PG Ⅱ,BRD4,and G-17 were signifi-cantly higher in the early gastric cancer group than in the non-gastric cancer group,while the level of pepsinogen(PG)Ⅰ was significantly lower(P<0.05).Logistic regression analysis revealed that preference for hot food,high-salt food,PG Ⅱ,BRD4,G-17,and PG Ⅰ were all influencing factors for Hp-positive early gastric cancer(P<0.05).The area under the curve(AUC)values for serum BRD4,G-17,and their combination in diagnosing Hp-positive early gastric cancer were 0.793,0.830,and 0.912,respectively.The diagnostic efficacy of the combined detection was superior to that of single detection(P<0.05).Conclusion The serum levels of BRD4 and G-17 are elevated in patients with Hp-positive early gastric cancer,and both exhibit certain diagnostic value for Hp-positive early gastric cancer,suggesting their potential as serum biomarkers for the diagnosis of Hp-positive early gastric cancer.
3.M2-TAMs-derived TGF-β1 inhibits CD8+T cell immune function and pro-motes progression of esophageal cancer
Sufang CHEN ; Yilin REN ; Kaige YANG ; Yuying JING ; Kai CHEN ; Yuyan DUAN ; Chenghua LUO ; Lianghai WANG ; Lan YANG ; Jianming HU
Chinese Journal of Pathophysiology 2025;41(5):851-860
AIM:To investigate the immunosuppressive effects of M2-like tumor-associated macrophages(M2-TAMs)on CD8+T cells within the tumor microenvironment of esophageal cancer.METHODS:Multiplex fluores-cence immunohistochemistry was used to analyze the distribution of immune cells in esophageal cancer tissues.An in vitro co-culture system was established,and flow cytometry along with Calcein-AM/PI staining was employed to assess the im-pact of M2-TAMs on CD8+T cell function.The GEPIA database was utilized to evaluate the prognostic significance of PDCD1 expression in esophageal cancer patients and to analyze the correlations between gene expressions.Immunohisto-chemistry(IHC)was performed to detect the expression of TGF-β1 in esophageal cancer tissues.Flow cytometry and en-zyme-linked immunosorbent assay(ELISA)were used to measure PD-1,IFN-γ and TNF-α expression in CD8+T cells fol-lowing treatment with a TGF-β1 inhibitor.RESULTS:Compared with early-stage(stage I)esophageal cancer patients,the patients with advanced disease(stages Ⅱ to Ⅳ)exhibited dynamic changes in the infiltration of CD4+T cells,CD8+T cells,Tregs,and M2-TAMs within tumor tissues,with significant correlations observed among these cell populations(P<0.05).The distribution of M2-TAMs and Tregs was positively correlated with poor prognosis(P<0.05),while that of CD8+T cells was negatively correlated(P<0.05).In contrast,CD4+T cell infiltration showed no significant association with clinical outcomes(P>0.05).Co-culture of CD8+T cells with M2-TAMs resulted in significant downregulation of CD107a,granzyme B,IFN-γ and TNF-α expression(P<0.01).Additionally,M2-TAM-treated CD8+T cells co-cultured with esophageal cancer cells led to reduced apoptosis of cancer cells.High expression of PDCD1 was significantly associated with poor prognosis(P<0.05),and significant correlations were observed between CD8A and PDCD1 expression,as well as between TGF-β1 and CD274 gene expression(P<0.01).TGF-β1 was also significantly associated with CD163+macro-phage infiltration and the progression of esophageal cancer(P<0.05).Treatment with a TGF-β1 inhibitor in the M2-TAM and CD8+T cell co-culture system significantly down-regulated PD-1 expression and increased the secretion of IFN-γ and TNF-α(P<0.01).CONCLUSION:The TGF-β1 derived from M2-TAMs inhibits the antitumor activity of CD8+T cells in the esophageal cancer microenvironment,suggesting potential therapeutic targets for overcoming immunosuppression in esophageal cancer.
4.M2-TAMs-derived TGF-β1 inhibits CD8+T cell immune function and pro-motes progression of esophageal cancer
Sufang CHEN ; Yilin REN ; Kaige YANG ; Yuying JING ; Kai CHEN ; Yuyan DUAN ; Chenghua LUO ; Lianghai WANG ; Lan YANG ; Jianming HU
Chinese Journal of Pathophysiology 2025;41(5):851-860
AIM:To investigate the immunosuppressive effects of M2-like tumor-associated macrophages(M2-TAMs)on CD8+T cells within the tumor microenvironment of esophageal cancer.METHODS:Multiplex fluores-cence immunohistochemistry was used to analyze the distribution of immune cells in esophageal cancer tissues.An in vitro co-culture system was established,and flow cytometry along with Calcein-AM/PI staining was employed to assess the im-pact of M2-TAMs on CD8+T cell function.The GEPIA database was utilized to evaluate the prognostic significance of PDCD1 expression in esophageal cancer patients and to analyze the correlations between gene expressions.Immunohisto-chemistry(IHC)was performed to detect the expression of TGF-β1 in esophageal cancer tissues.Flow cytometry and en-zyme-linked immunosorbent assay(ELISA)were used to measure PD-1,IFN-γ and TNF-α expression in CD8+T cells fol-lowing treatment with a TGF-β1 inhibitor.RESULTS:Compared with early-stage(stage I)esophageal cancer patients,the patients with advanced disease(stages Ⅱ to Ⅳ)exhibited dynamic changes in the infiltration of CD4+T cells,CD8+T cells,Tregs,and M2-TAMs within tumor tissues,with significant correlations observed among these cell populations(P<0.05).The distribution of M2-TAMs and Tregs was positively correlated with poor prognosis(P<0.05),while that of CD8+T cells was negatively correlated(P<0.05).In contrast,CD4+T cell infiltration showed no significant association with clinical outcomes(P>0.05).Co-culture of CD8+T cells with M2-TAMs resulted in significant downregulation of CD107a,granzyme B,IFN-γ and TNF-α expression(P<0.01).Additionally,M2-TAM-treated CD8+T cells co-cultured with esophageal cancer cells led to reduced apoptosis of cancer cells.High expression of PDCD1 was significantly associated with poor prognosis(P<0.05),and significant correlations were observed between CD8A and PDCD1 expression,as well as between TGF-β1 and CD274 gene expression(P<0.01).TGF-β1 was also significantly associated with CD163+macro-phage infiltration and the progression of esophageal cancer(P<0.05).Treatment with a TGF-β1 inhibitor in the M2-TAM and CD8+T cell co-culture system significantly down-regulated PD-1 expression and increased the secretion of IFN-γ and TNF-α(P<0.01).CONCLUSION:The TGF-β1 derived from M2-TAMs inhibits the antitumor activity of CD8+T cells in the esophageal cancer microenvironment,suggesting potential therapeutic targets for overcoming immunosuppression in esophageal cancer.
5.Expression of alcohol dehydrogenase 1 A and vascular endothelial growth factor-A in hepatocellular carcinoma
Lele XUE ; Yuying JING ; Kaige YANG ; Liwen QI ; Tong WU ; Yilin REN ; Yichen ZANG ; Lianghai WANG ; Haijun ZHANG ; Weihua LIANG ; Jianming HU
Acta Universitatis Medicinalis Anhui 2024;59(3):499-505
Objective To investigate the expression,synergistic relationship and clinical significance of alcohol de-hydrogenase(ADH1A)and vascular endothelial growth factor-A(VEGFA)in hepatocellular carcinoma(HCC).Methods The expression and correlation of ADH1A and VEGFA in HCC and adjacent normal tissues were ana-lyzed by GEPIA.TCGA and GSEA were used to analyze the pathway of ADH1A in HCC.The clinical and patho-logical data of 84 patients with HCC were collected,and 54 patients with paracancer normal tissue samples were se-lected as controls to analyze the correlation between ADH1A and VEGFA and clinicopathological parameters of HCC.Immunohistochemistry was used to detect the protein expression of ADH1A and VEGFA in cases and con-trols,and the correlation between the expression of ADH1A and VEGFA and the clinical progression and prognosis of patients with HCC was analyzed based on clinical pathological parameters and Kaplan-Meier.Results Bioinfor-matics analysis found that ADH1A was low-expressed in HCC and VEGFA was highly expressed in HCC,and there was a negative correlation between the two(P<0.001);immunohistochemical detection results showed that the expression of ADH1A in HCC tissue was lower than that in normal tissue adjacent to cancer(P<0.01)while the expression rate of VEGFA in HCC tissue was significantly higher than that of normal tissue adjacent to cancer(P<0.01);The recurrence rate of vascular thrombus and HCC patients in HCC group with high expression of ADH1A was lower(P<0.05).The proportion of tumor diameter>5 cm,high TNM stage,microsatellite and G2-G3 dif-ferentiation in HCC tissues in VEGFA high expression group was higher(P<0.05).Kaplan-Meier survival analy-sis showed that patients with high ADH1A expression and low VEGFA expression had a higher five-year survival rate.Conclusion Low expression of ADH1A and high expression of VEGFA in tumor tissues of patients with HCC indicate tumor progression and can be used as one of the prognostic evaluation indicators for patients with HCC.
6.Analysis of inflammatory factors and BDNF expression in the brain hippocampus of Alzheimer's disease-like mice caused by Aβ25-35
Wen LU ; Jinye REN ; Xiangwei HE ; Liang TANG ; Jianming LI
Chongqing Medicine 2024;53(5):657-663
Objective To investigate the expression of inflammatory factors and brain-derived neurotro-phic factor(BDNF)in the brain hippocampus of Alzheimer's disease(AD)-like mice caused by amyloid β-protein 25-35(Aβ25-35).Methods A total of 40 six-week-old male Kunming mice were taken to construct an AD-like mouse model using bilateral ventricular injection of Aβ25-35,and were divided into the 0 d,7 d,14 d,and 28 d groups for observation,with 10 mice in each group.The Y-maze and new object recognition assay were used to test the learning and memory functions of the mice.The hematoxylin-eosin(HE)staining was used to observe the neuronal damage in the hippocampal region.Immunohistochemical staining was used to detect the expression levels of phosphorylated-tau(p-tau),CD11b and BDNF in hippocampus.ELISA was used to detect the expression levels of inflammatory factors in hippocampus,including interleukin-1β(IL-1β)and tumor necrosis factor-α(TNF)-α,and real-time quantitative reverse transcription PCR(RT-qPCR)and Western blot were used to detect the mRNA and protein expression levels of BDNF.Results Aβ25-35 could impair memory and cognitive function in the mice.Compared with the 0 d group,the neuron number in the hippocampal tissue of mice in the 14 d and 28 d groups was significantly reduced(P<0.05),and the optical density values of p-Tau and CD11b,and expression levels of IL-1β and TNF-α in the hippocampal region of mice in the 14 d and 28 d groups were significantly increased(P<0.05).In addition,compared with the 0 d group,the relative expression levels of BDNF mRNA and protein in the hippocampal tissue of mice were sig-nificantly increased in the 7 d group(P<0.05),while the relative expression levels of BDNF mRNA and pro-tein were significantly decreased in the 14 d and 28 d groups(P<0.05).Conclusion Aβ25-35 may increase the expression of TNF-α,IL-1β and p-tau in hippocampal tissue by activating microglia,which in turn impaired the memory and cognitive functions of mice,and the expression level of BDNF in hippocampal tissue showed a first increase and then a decrease in the injury period.
7.Gastrin-releasing peptide receptor targeted PET imaging of 68Ga-DOTA-PEG 4-BBN for prostate cancer
Jiaqi YUAN ; Yaxi LI ; Dujuan LIU ; Ran REN ; Menglu LI ; Ninghan FENG ; Jianming NI
Chinese Journal of Nuclear Medicine and Molecular Imaging 2024;44(5):303-308
Objective:To design and develop a molecular imaging probe of 68Ga-labeled bombesin (BBN) analogue, 68Ga-1, 4, 7, 10-tetraazacyclododecane-1, 4, 7, 10-tetraacetic acid (DOTA)-polyethylene glycol (PEG) 4-BBN, and investigate its potential to target prostate cancer with high expression of gastrin-releasing peptide receptor (GRPR) while minimizing uptake in pancreatic tissue. Methods:Based on the amino acid sequence of BBN peptides, the precursor DOTA-PEG 4-BBN was designed and prepared, followed by labeling with 68Ga and conducting to quality control analysis. The tumor uptake of 68Ga-DOTA-PEG 4-BBN was assessed by microPET/CT imaging on tumor-bearing nude mice models with PC3 of high GRPR expression or HT29 of low GRPR expression (3 mice per group). 68Ga-DOTA-PEG 4-BBN microPET/CT imaging was also performed on 6 tumor-bearing nude mice models with PC3, among which 3 mice were treated with gastrin-releasing peptide antagonist 1 h prior to injection of the tracer (blocked group). After imaging, the ex vivo tissues of 3 PC3 tumor-bearing nude mice of the non-blocked group were examined for radioactivity counting to evaluation the biodistribution of 68Ga-DOTA-PEG 4-BBN, and the percentage injected dose per gram of tissue (%ID/g) was calculated. Independent-sample t test was used for data analysis. Results:The synthesis of 68Ga-DOTA-PEG 4-BBN took 40 min, with the radiochemical yield of 50%-60% (no decay correction) and the radiochemical purity of over 95%. After incubation in the serum at 37 ℃ for 4 h, the radiochemical purity remained more than 95%. The microPET/CT imaging results indicated that the uptake in the PC3 tumor was 3.2 times higher than the uptake in the tumor after GRPR blockade ((1.34±0.24) vs (0.42±0.03) %ID/g; t=5.47, P=0.005). After the injection of 68Ga-DOTA-PEG 4-BBN at 1 h and following imaging for 15 min, the PC3 tumor-bearing nude mice models of the non-blocked group showed that the pancreatic uptake ((0.150±0.058) %ID/g) was significantly lower than that in kidneys, lungs and liver ((9.452±0.234), (0.720±0.041), (1.572±0.213) %ID/g) with a profound statistical distinction ( t values: 11.28-53.02, all P<0.001). The tumor/pancreas uptake ratio could reach 16.92 in the tumor-bearing nude mice models with high GRPR expression. Conclusion:A novel molecular imaging probe 68Ga-DOTA-PEG 4-BBN demonstrates specific recognition of tumors with high GRPR expression while exhibiting low uptake in the pancreas, which shows its potential in prostate cancer molecular imaging.
8.Bioinformatics analysis based on effect of M2 macrophage-derived Siglec15 on malignant biological behaviour of esophageal squamous cell carcinoma cells and its experimental validation
Yilin REN ; Yichen ZANG ; Lele XUE ; Kaige YANG ; Sufang CHEN ; Weinan WANG ; Chenghua LUO ; Weihua LIANG ; Lianghai WANG ; Feng LI ; Jianming HU
Journal of Jilin University(Medicine Edition) 2024;50(4):881-890
Objective:To discuss the effect of sialic acid-binding immunoglobulin-like lectin-15(Siglec15)derived from M2 tumor-associated macrophages(M2-TAMs)on promoting the malignant biological behavior of the esophageal squamous cell carcinoma(ESCC)through bioinformatics analysis,and to validate the findings through cell experiment.Methods:The Tumor Immune Estimation Resource(TIMER)online Database was used to analyze the expression differences and immune infiltration of Siglec15 in pan-cancer and adjacent normal tissues.Real-time fluorescence quantitative PCR(RT-qPCR)method was used to detect the expression levels of Siglec15 mRNA in M2-TAMs and ESCC EC109 and KYSE150 cells.Based on the non-contact co-culture of M2-TAMs and ESCC cells,the following groups were set up,such as EC109/KYSE150 group,EC109/KYSE150+si-NC group(transfected with si-NC sequence),and EC109/KYSE150+si-Siglec15 group(transfected with si-Siglec15#1 and si-Siglec15#2 sequences).CCK-8 method was used to detect the proliferation activities of the cells in various groups;wound healing assay was used to detect the wound healing rates of the cells in various groups;Transwell chamber assay was used to detect the numbers of migration and invasion cells in various groups;flow cytometry was used to detect the apoptotic rates of the cells in various groups.Results:The bioinformatics analysis results showed that compared with adjacent normal tissue,the expression levels of Siglec15 mRNA in pan-cancer tissues such as esophageal cancer,colon cancer,and head and neck squamous cell carcinoma tissues were increased(P<0.05 or P<0.01),and the expression level of Siglec15 mRNA in esophageal cancer tissue was significantly positively correlated with the infiltration of the macrophages(P<0.05).Compared with the EC109 cells and KYSE150 cells,the expression level of Siglec15 mRNA in M2-TAMs was significantly increased(P<0.01).There was no significant difference in the proliferation rate of the cells among EC109/KYSE150 group,EC109/KYSE150+si-NC group,and EC109/KYSE150+si-Siglec15 group(P>0.05).Compared with EC109/KYSE150 group,after treated for 24 and 48 h,the wound healing rate of the cells in EC109/KYSE150+si-NC group was increased(P<0.01),the numbers of migration and invasion cells were increased(P<0.05),and the apoptotic rate was decreased(P<0.01).Compared with EC109/KYSE150+si-NC group,the wound healing rates of the cells in EC109/KYSE150+si-Siglec15#1 group and EC109/KYSE150+si-Siglec15#2 group were decreased(P<0.05),the numbers of migration and invasion cells were decreased(P<0.05),and the apoptotic rates of the cells had no significant difference(P>0.05).Conclusion:Siglec15 derived from M2-TAMs may be a key factor in promoting the migration and invasion of the ESCC cells.
9.Propionic and butyric acid levels can predict ability in the activities of daily living after an ischemic stroke
Hankui YIN ; Zhongli WANG ; Ming ZENG ; Ming SHI ; Yun REN ; Linhua TAO ; Yunhai YAO ; Jianming FU ; Xudong GU
Chinese Journal of Physical Medicine and Rehabilitation 2024;46(7):631-634
Objective:To seek a correlation between short-chain fatty acids (SCFAs) and skill in the activities of daily living (ADL) after an ischemic stroke.Methods:Ninety ischemic stroke survivors were assessed using the Barthel Index (BI). Fecal samples were collected and analyzed for the concentration of acetic acid, propionic acid, butyric acid, isobutyric acid, valeric acid, and isovaleric acid using gas chromatography. Spearman correlation analysis was conducted to identify SCFAs that correlated with the total BI score. Linear regressions were evaluated to explore the correlation between the total BI score and SCFAs.Results:The concentrations of propionic and butyric acids in the feces were found to correlate significantly with the total BI scores. Data including propionic acid and butyric acid levels, age, gender, body mass index, disease duration, any history of hypertension or diabetes, and other SCFAs were included in the regression models. Propionic and butyric acid levels were found to be potentially useful predictors of total BI scores.Conclusions:The concentration of propionic and butyric acids in the feces after an ischemic stroke can predict the survivor′s total BI score. Those concentrations could therefore be useful for predicting ADL ability.
10.Effect of high-frequency repetitive transcranial magnetic stimulation on hemiplegic shoulder pain during convalescence of stroke
Linhua TAO ; Zhibin REN ; Xiaoqian FU ; Liang LI ; Yueli WANG ; Jianming FU
China Modern Doctor 2023;61(35):37-41
Objective To observe the effect of high-frequency repetitive transcranial magnetic stimulation on hemiplegic shoulder pain during convalescence of stroke.Methods A total of 40 patients with hemiplegic shoulder pain during convalescing stroke who were hospitalized in Rehabilitation Medicine Department of Jiaxing Second Hospital from January 2021 to June 2022 were selected and randomly divided into treatment group(rTMS group)and control group(sham rTMS group),with 20 cases in each group.Both groups were given anti-inflammatory and analgesic drugs and conventional rehabilitation treatment.On this basis,the treatment group was combined with rTMS treatment(stimulation frequency was 10.0Hz,stimulation intensity was 80%resting motor threshold,stimulation time was 10s,interval was 50s,total treatment time was 20 minutes,once a day from Monday to Friday,continued treatment 2 days apart,20 times as a course of treatment,a total of 4 weeks),while the control group received sham rTMS.Before treatment,2 and 4 weeks after treatment,numerical pain rating scale(NPRS)was used to assess the degree of shoulder pain,passive shoulder range of motion was measured by protractor,upper limb motor function of hemiplegic side was assessed by Fugl Meyer assessment upper extremity(FMA-UE),and the ability of daily living activities was assessed by modified Barthel index(MBI).Results After treatment,NPRS score of shoulder pain in 2 groups was significantly decreased compared with before treatment(P<0.001),passive shoulder motion and Fugl-Meyer upper limb motor function were significantly improved compared with before treatment(P<0.001),and the treatment group was significantly better than the control group,the difference between groups was statistically significant(P<0.05).The modified Barthel index in 2 groups was significantly improved compared with before treatment(P<0.001),but there was no statistical significance between 2 groups(P>0.05).Conclusion 10.0Hz high-frequency repetitive transcranial magnetic stimulation can significantly relieve hemiplegic shoulder pain during the convalession of stroke,improve the passive range of motion of the affected shoulder,and improve the upper limb motor function of the affected side,but the effect is not significant in improving the ability of daily living activities.


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